Uncle Pein
by purple-square-Q-9-3
Summary: What would happen if Jiraiya found the ame orphans after training Minato, and brought them to Konoha, and Nagato found a living family member, his big sister Kushina. Read how things could've panned out if things happened differently, and some family trees were different. Strong Naruto since he has a proper guardian. Rated M in case
1. Prologue

**AN/Synopsis: I suggest that you read this before reading the main story since it will help you to understand my train of thought since this fic took some serious thought to put together. I noticed a pretty big inconsistency within the Naruto timeline. The inconsistency involves the Ame orphans and their age in relation to Naruto's parents' ages. In the anime and manga we are at least led to believe that Jiraiya leaves them about when they are Genin age (12-14) after training them for three years and then later on he trains the Fourth Hokage starting when Minato is 12, this couldn't work as the Ame orphans are 4.5-5 years younger than the Fourth Hokage. This is according to the data books. Nagato and Konan are 35 during the Pein fight arc while Naruto is 16 basic math indicates that they would be roughly 19-20 when Naruto was born, while Naruto's parents are 24 at time of death (AKA the night Naruto is born) and would've been 40 when they appeared in the cannon series if they had lived. So this fic is mostly how I think things would've actually worked if the If Jiraiya had found the Ame orphans after training Minato instead of before. As for making Nagato Kushina's little brother it only says that he lived with family and even on the wiki it says that they are presumably his parents with no confirmation which doesn't mean it's impossible, also this is fanfiction and I do what I want. Also I figured since I'm saving the Ame orphans, and Yahiko resembles Jugo enough for them to at least be from the same clan, having the same hair, skin, and eye color (eye color is kind of iffy since Yahiko and Jugo have different eye colors in the manga than the anime, and Yahiko is only ever seen alive in low light, but in low light their eyes look the same at least in the anime), so at some point Yahiko will start using Jugo's Kekkei Genkai. These aren't the only family trees that are getting fiddled with, the rest however are going to be revealed to the readers as the story progresses.**

* * *

Prologue

* * *

"Well kids, I think I've taught you enough to survive. You're all thirteen now, that's official shinobi age, and I hate to say this, but it's hig8h time I get back to Konoha." Jiraiya says to the three orphans that he's been taking care of and teaching to live for three years. "Besides I think it's time for you to pursue your own goals." He continued.

The children in question simply stared at him before trying not to break into tears

"Sensei please take us with you. This land is war-torn and almost completely destroyed, we'd be much better off Konoha with you, even if it's the village that caused a lot of this destruction." Konan pleaded not wanting to live on the streets again.

"She's right, though I can't speak for Nagato since Konoha shinobi killed his aunt and uncle, I'd like to live in the village you come from, it sounds like a nice enough place. I would rather not live on the streets here if possible." Yahiko said looking at his best friend and rival.

"If I hold a grudge against an entire village for the actions of two likely dead men, then that would make me a serious hypocrite. I look to bring about peace and end the cycle of hatred. Honestly I'd rather have the backing of a major shinobi village than try it as a random group of teenagers that have basic knowledge of ninja arts." Nagato said standing from his seat. "Jiraiya sensei please allow us to accompany you to Konoha and live there. Besides if anyone from Uzu survived the attack I believe that that's where they would've ended up. Maybe I have family there."

"Well fine I'll take you with me, though it's up to my sensei whether or not you can stay. He is after all the Hokage. His word is law." Jiraiya says. "Pack your stuff, we leave in two hours."

The trip was not a quiet one. The orphan trio continuously speculating on how life inside a large thriving village would be. The three were understandably nervous, yet excited. Even living on the streets of Konoha would be an improvement to their life in Ame if they had stayed. As they crossed the border into Hi no Kuni the sun was so bright that they had to stop for a moment and let their eyes adjust to the light.

"It's so beautiful here. The blue sky, the trees, the sunlight. It's all a bit much to take in coming from a country where everything but the people is grey." Yahiko says earning confirming nods from his fellow orphans.

"Remember Nagato keep your eyes covered until we talk to the Hokage." Jiraiya said earning a nod from the boy.

The rest of the trip after that comment got quiet as the orphans soaked in the scenery of the land they hoped to call home soon. Jiraiya sent a messenger toad ahead of them to alert the Hokage of their imminent arrival in order to avoid any misunderstanding.

As they approached the village gates they were greeted "Jiraiya Sensei! How's it going? We heard you were on your way with company so we volunteered to serve as your escort to the Hokage's office." A tall blond young man of 18 standing with two rather stoic figures of the same age shouted at the group.

"Well will you look at that? The team's back together, after our trip to the Hokage's office we should go for some Ramen and catch up." Jiraiya said to the three as they entered the village.

"I can't after this I have a date to get to, and my girlfriend is the last person I want to piss off." The boy said scratching the back of his head and smiling.

"Really a date? Who with? Come on Minato give me some details here." Jiraiya's curiosity decided to show itself.

"You remember Tsunade's former student Kushina right?" Minato said noticing Nagato perk up upon hearing the name.

"You mean to tell me that you're dating the Red Hot-Blooded Habanero. How the hell did this happen?" Jiraiya was even more curious now.

"Well about a year and a half age she was kidnapped by five Kumo shinobi. She left a trail made of her hair and I followed it, I one of my new techniques to dispatch the kidnappers. When she asked me how I found them I told her that I followed her beautiful red hair, and we kissed. We later decided that it was likely a heat of the moment thing, but we decided to give dating a try, we've been dating ever since." Minato said giving the really short version of the story. "Come to think of it she told me that the Hair is a clan thing, this kid looks like he could be her brother." Minato continued while pointing at Nagato.

"Maybe. Last I heard my ne-chan was on her way here, but got attacked by bandits and killed along with Oka-san. Funny how even the third strongest ninja in a village can be killed by common bandits when they get careless. The only reason that I doubt that it's her is there were quite a few Kushinas in our age group in Uzu." Nagato said looking at the ground.

"Well I'll talk to sensei and see if some bloodwork can answer that debacle." Jiraiya says scratching his head.

"I'll send Kushina a toad telling her that I'll be late, she won't like it. But I think the sight of a cousin, or possibly even brother, along with my other surprise will more than make up for it." Minato said summoning a small toad and giving it instructions to seek out Kushina and tell her that he'll be late and that he'll give his reasons when they meet up.

"So Fugaku, Hiashi, what's new. Don't tell me that you two have girlfriends as well." Jiraiya wanted to know what his former students were up to.

"Well I made Jonin like Minato-san. And I have recently began courting Hitomi. Though my story is much less interesting than Minato-san's. We simply had mutual interest in each other and began courting as per the standard." Hiashi said showing no emotion in his face.

"I as well am now a Jonin, I will likely be clan head by years end due to my father's condition worsening. Not even Tsunade-sama can diagnose his illness, let alone treat it. And I also now have a romantic partner. Mikoto from Tsunade-sama's team will make a great wife, and mother someday in the future." Fugaku said remaining just as stoic as his longtime rival.

"Well I'll be damned. All of my team getting together with all of Tsunade's team. Who would've thought? Now if only Tsunade would finally realize that I'm not joking when I say that I've had feelings for her since we were Genin it would all be complete." At this point the group of seven had arrived at the Hokage tower. "Well this is our stop, I'll talk to you guys later when we can all meet up and go for ramen or something and catch up in more detail. Minato you should come with us. You are after all going to be waiting till we're done anyway. And the only secret will come after Nagato moves his hair." Jiraiya said whispering the last sentence in Minato's ear.

"Okay sensei." Let's go.

The way from the entrance to the Hokage's office was quiet with no words spoken. All present could feel how nervous the three orphans were.

Jiraiya opened the door to the Hokage's office saying "Sensei I'm home, and the three children behind me are the three orphans I stayed behind to train. Nagato apparently he's an Uzumaki, Konan, and Yahiko."

"Yes that one does resemble an Uzumaki. Do the other two have clans?" The third Hokage asked him.

"Not that we're aware of. Though that doesn't mean it's out of the realm of possibility. Konan developed jutsu revolving around paper, and Yahiko seems to absorb small quantities of Nature energy when his chakra is low. Now on to Nagato, I think that for this part it should be just us, the kids, and Minato." Jiraiya said getting incredibly serious with the last sentence.

"Before that, since they are here of their own free will I must ask. Why not just bring them here in the first place?" The third Hokage asked his former student.

"I didn't expect them to want to come here otherwise I would've just brought them here. Their parents and guardians were confused by Konoha shinobi for enemies and killed by them. Initially they didn't even trust me, being from Konoha this was understandable. I don't know when during the time we spent together they changed their minds, if I did we would've returned then rather than now." Jiraiya said before the Hokage waved his hand causing the ANBU present to exit the room.

"What about that boy is so special, and why trust Minato over my ANBU?" The Hokage wanted answers.

"Well we don't know if any of those ANBU are with Danzo, and Minato's one of the favored candidates for Hokage when he comes of age. Now as for what's so special, Nagato, show them your eyes." The boy did as instructed.

The Hokage and Minato gasped upon seeing his eyes.

"Is that what I think it is?" The Hokage asked jumping over his desk, scattering the paperwork, and grabbing Nagato's face. He then proceeded to turn his face examining the boy.

"Yes, that's the genuine Rinnegan. This surprised me as well when it awakened. I thought Kushina's chains were the Uzumaki Kekkei Genkai, but now, after learning that he is also an Uzumaki, I'm starting to wonder if they have two. Or maybe it's something more. We'll talk more about that later. My only concern is that he doesn't seem to be able to deactivate it. I mean it doesn't drain his chakra by simply being active, but it would be hard to explain if we had a kid walk around the village with the Rinnegan active." Jiraiya said scratching his chin deep in thought.

"Before we get too far off base according to Nagato he had a sister named Kushina, and he might be referring to my Girlfriend. Standard procedure for this situation dictates we have all three new village entries undergo bloodwork to see if they have any relatives in the village since they're orphans. I think we should do this as quickly as possible." Minato piped up reminding the others in the room the main purpose of the meeting.

"Yes we must get to that as soon as possible. For now, Nagato, use a Henge to hide your eyes. We'll find a better solution to this predicament later." The third Hokage said before letting go of Nagato and leading the group to the hospital to get the necessary bloodwork and exams done.

* * *

A few hours later

* * *

"Well Nagato, according to this chart your DNA is similar enough to Kushina Uzumaki to suggest that you share at least one parent. So in short she is indeed your sister. Other than that you are a little physically weaker than the typical Genin, but that can be fixed by adjusting your diet, and doing some more physical training. Your chakra reserves however are damn near off the charts." Minato said reading the results to the boy since the doctor had been called to a different patient whose life was in danger.

"So ne-chan is alive." Nagato was dumbstruck to say the least.

"Well that's all we need here for now. Let's get the others and go meet her, I'm sure she'd like to see you after all these years." Minato said putting the chart down and offering Nagato a hand.

"What if she doesn't remember me? What if it's awkward? What if the tests were wrong? I don't know about this." Nagato said obviously worried about talking to his sister for the first time in eight years.

"Well then we'll see when we get there. Come on Nagato even if she is just your cousin that's better than not having family period." Minato said helping him off of the exam table.

"That doesn't make me feel any better. I don't know what I'd do if the tests lied, I just don't want to get my hopes up for nothing." Nagato said with a frown.

"We'll see about that, first let's go see her. She's probably ready to tear my head off as it is." With that they gathered the other two orphans and left.

* * *

Several minutes later

* * *

Minato sent a toad to tell Kushina were to meet him and to be ready for two major surprises. He sat next to Nagato and the Ame orphans at Ichiraku Ramen. Nagato was wearing a traveler's hood in order to conceal his identity until Minato gave him the signal to reveal himself.

Kushina was fuming when she arrived. "You'd better have a damn good reason for postponing our date, dattebane!"

"Some business revolving around Jiraiya sensei's arrival kept me. These are the three orphans that Jiraiya has been looking after for the past three years. I decided to treat them to a meal before we figure out living arrangements for them. It seems that only one of them has a living relative in the village." Minato said while pointing at the trio.

"Oh yeah. Which one?" Kushina asked.

"Nagato you can take off the hood." Nagato removed his hood and turned to face Kushina causing her eyes to widen as if she'd seen a ghost.

"Nagato. Ototo." After saying this Kushina tackle hugged the boy so hard that he fell off the stool he was sitting on. "I thought you died when Uzu fell." Kushina was crying tears of joy while Nagato's face began to turn blue from lack of oxygen as he tried to return the hug.

"Kushina, you might want to loosen your grip, or else he might actually die from asphyxiation." Minato said both smiling and sweat-dropping.

"Oh Kami you've grown so much! Last time I saw you, you were just a cute little five year old." Kushina had allowed him to breathe, but was still smothering him with affection. He reached out toward Minato, his hand twitching. Minato could've sworn he heard the words 'help me' just before his Henge popped. Kushina felt the technique release and looked up only to notice nothing had changed except now the boy's bangs now covered his eyes. She tried to move them aside but found that Nagato was using the chakra sticking method to keep them there. "What are you hiding? It's not a hideous scar is it? Who hurt my Ototo? I'll kill them, dattebane!" Her hair started to form her trademarked 'tails' that put fear into the hearts of many.

"Kushina! Calm down it's not a scar. It is however something that can't be shown in public. Nagato resume the Henge, we'll show your sister later in private, now I think introductions are in order. Yahiko, Konan, this is Kushina Uzumaki, Nagato's long lost sister, Jonin of Konoha, and my girlfriend." The orphans nodded and waved when their names were mentioned.

"Nice to meet you Kushina-san" Konan said before creating a bouquet of paper flowers and handing them to Kushina.

"Don't mind her, it's just her way of extending the hand of friendship, kind of like a handshake. She can be a little weird like that." Yahiko said while staring at the menu.

"Well then, thank you Konan. So you guys have been living with Nagato-kun for a while now." An awkward silence fell upon the group that lasted for almost a minute before Kushina tried again. "Do any of you have any clue where you are going to stay?"

"We'll figure something out, we always have. Even if we live on the streets it'll be an improvement from Ame. At least here the weather is nice." Yahiko said trying to reassure himself more than anyone else.

"Well, if you can't find a place to stay, I've got open rooms that you could use until you can find a place to stay." Minato said throwing out the offer.

"Minato, did you hit your head or something? Last time I checked you lived in a one bedroom apartment like me." Kushina was earnestly confused.

"Well that's something I wanted to talk to you about. We've been dating for more than a year, I was kinda wondering if you wanted to move in with me? I bought a four bedroom house earlier this week." Minato was acting kind of shy, Kushina found this to be cute.

"Minato, I would love to move in with you. But first, why four bedrooms?" Kushina already knew the answer, but she wanted to hear Minato say it anyway.

"In case of family expansion, you know, kids." Minato was blushing furiously when he said this, as they have yet to even perform the act required in order to make children. Let alone plan for what to do if they had little ones running about.

Kushina pulled him into a kiss a few seconds after he finished speaking. It was brief since they were in public, PDA wasn't really their thing.

"Well let's eat, then we can figure everything out later. I figured that I'd at least extend the offer." Minato said before ordering

* * *

 **AN: That's it for now. Tell me what you think so far. Am I doing good? Should I continue, or should I make this fic disappear? I really want to know what you people think. Anyway leave a review answering these questions, and I'll see you next time, if you stick around that is.**


	2. Event's Changed

**AN:This chapter is all about things that changed before Naruto's birth. You could almost call it the second part of the prologue.**

* * *

2 years until Kyubi attack

* * *

Minato sat on him and Kushina's bed channeling chakra into her seal in order to repair the damage done to it during the day. This had become a nightly routine ever since Kushina had seen Nagato's Rinnegan. The beast within the seal went ballistic shouting about how impossible for anyone to have those eyes, and was fighting to escape with more vigor than ever. He demanded blood, it effected Kushina's abilities in the field drastically. It was already hard enough to contain the strongest Biju in the midst of battle, but now that it was more pissed off than usual it was damn near impossible. Along with the fact that Konoha is at war right now doesn't bode well for the kunoichi.

"Ne-chan, I think it's about time that the Kyubi and I bury the hatchet. I don't know what its problem is, but this is getting ridicules." Nagato said walking through the open door to the couple's room. He was now tall for a seventeen year old, while he was now in better physical condition he was still scrawny.

"No, you are not entering my mindscape and that's final." Kushina had heard this before, and every time she gave a similar response.

"Sorry Ne-chan, but this time you don't have much of a choice. The Kyubi is killing you, maybe not directly, but if you continue to fight with it going crazy like this you aren't going to make it to you and Minato's wedding. I'm sorry, but you have to understand that this is for your benefit." Nagato said before she felt a blow to the back of her neck, and passed out. "Minato-san, you know the drill, I just hope that she can forgive us for this." Nagato said activating the powers of the Human path to force his way into his sister's mind.

* * *

In Kushina's mindscape

* * *

"Alright Furball what's your problem with me and my eyes?" Nagato asked in a cocky tone as he put Kushina in a clear dome structure to prevent her from screaming, or trying to expel him from her head.

 **"** **You dare to speak to me, the Kyubi no Yoko, as if I'm some common house pet! I can't wait to pulverize you in between my fingertips!"** The Kyubi started struggling more fiercely than before to break free.

"Answer my question before I rip your memories out and find out for myself! I don't know what your problem is, but it's putting my sister in danger. If she dies I'll track you down when you reform. I'll personally seal you onto a rock that's reinforced with more seals to prevent your escape, and that's where you will remain for all eternity. You think that this seal is uncomfortable, wait until it doesn't have senses for you to experience." Nagato was blaring killing intent on par with the Biju at this point.

 **"** **Shut up you mongrel! You may have his eyes, but you can't compare to my father who could actually follow through with the threat you just made!"** The Kyubi managed to get a single tail free for a short period of time before it was staked back to the boulder he was strapped to.

"The Rikudo Sennin was your father!? Wait, You have a father?!" Nagato was surprised to say the least.

 **"** **Why do I even bother communicating with you Ningen?"** The Kyubi seemed to calm down at Nagato's childish outburst.

"Seriously why do you want me dead so bad? I didn't do anything to you. I just want to protect my Ne-chan." Nagato was hoping that since the Kyubi had calmed down he could get an answer finally.

 **"** **Tell me Ningen, what's your goal in life?"** Nagato wasn't expecting the Kyubi to ask him a question

"Why do you want to know?" Nagato asked in response.

 **"** **TELL ME! I refuse to speak further until you tell me Ningen**." The Kyubi shouted.

"My goal is to end all wars, unite the five great nations, and create a world where Jinchuriki aren't needed. A world where people don't have to watch their family slaughtered for being mistaken for enemy soldiers, a world where fear won't lead to the eradication of a country simply because they don't choose a side in a war. I'll break the cycle of hatred that's taken hold of this world." Nagato said with conviction.

 **"** **You aren't lying, but how do you plan to bring this world without wars you speak of about? How do you plan to bring about the peace that you seek?"** The Kyubi asked.

"Peace… I don't know how to get there… but… but someday I'll break the curse. If there's such a thing as peace, I will find it!" Nagato said the same thing that he'd told Jiraiya a few years ago when he asked a similar question. "These eyes of mine let me into the minds and hearts of people, so that's a start."

 **"** **Boy your eyes do more than that. The power you contain could bring this planet to its knees if used for that purpose. I wanted to kill you so that you didn't use my father's power for evil and taint his legacy. Tell me, which is more important in the quest for peace, love or power?"** The Kyubi continued asking his questions.

"I don't know. Love is important, but you need power to protect the peace from those who would seek to destroy it. I guess that both are equally important." The Kyubi stopped struggling after hearing this.

 **"** **Boy you've just earned my approval, don't disappoint me. If you do then you and your entire race will regret it. Have a seat we have much to discuss about your eyes, and please call me Kurama."** The Kyubi surprised Nagato and Kushina for the second time that day when he smiled and gave out his real name.

* * *

1 year until Kyubi attack

* * *

"Okay team Kakashi, your mission is to destroy the bridge our enemy needs for their supply lines. Expect minor resistance, most of their forces are on the front lines, but it would be foolish to leave a bridge that important undefended." Minato said pointing at a map indicating the position of their target.

"Hai sensei!" Kakashi, Obito, and Rin said in unison.

"After your target is destroyed retreat immediately, team Ame is on their way to assist you in your escape. I'll accompany you guys to the border, after that I have to go back to the frontlines. Kakashi is the leader of this operation."

* * *

Several hours later.

* * *

"They've got Rin, We've got to go after them!" Obito said after a short encounter with two enemy Jonin that beat him and Kakashi, and kidnapped Rin.

"No. We continue the mission. She's a medic nin so even as a prisoner she'll be treated well." Kakashi said emotionlessly.

"She's our teammate! And she's a female, they'll probably rape her endlessly despite the fact that she's a medic nin. I'm not going to let that happen!" Obito was angry to say the least.

"We have our orders. Shinobi who disobey orders are trash." Kakashi said sternly.

"Then I'll gladly become that kind of trash. I still to this day think that the White Fang is a hero. Those who disobey orders are trash, but those who abandon their comrades are worse than trash. I don't care if you're leader, I'm going to save the woman I love from a fate worse than death. If you want to join me then fine, if not then just go away!" Obito turned around and began to walk away. Kakashi was astonished that anybody thought of his father in a positive manner, and was beginning to question his beliefs in the rules.

"So Rin got captured?" A new voice said as three cloaked figures landed between the two arguing boys.

"Yeah, I'm going to go get her. You got a problem with that Sempai?" Obito said to the figure that asked.

"No, but I do have one question. What the hell are we waiting for? We've got a rescue to mount!" Nagato said removing his hood, as did the two with him revealing Yahiko, and Konan.

"Right Sempai they went this way." Obito and team Ame left to pursue the kidnappers, leaving Kakashi to ponder for a while before he too turned to follow them.

* * *

At the enemy base

* * *

Each of the four Konoha shinobi there to Rescue Rin were stationed in different positions around the Earth Dome that the Iwa nin were using as a base.

"Okay we can do this. I can do this. I going in." Obito said to motivate himself.

"Going into where exactly?" A voice asked behind him.

Obito turned around only to see nobody was there. That's when he felt something impact against his stomach knocking the wind out of him. The Iwa nin that snatched Rin earlier then appeared, he had been using a Genjutsu to become invisible.

'Shit! I'm going to die here, and I haven't even told Rin how I feel yet.' Obito was thinking this when Kakashi roundhouse kicked the Iwa nin into the trunk of the tree that they were standing on.

Kakashi then charged his Chidori and charged at the Iwa nin, he missed his mark grazing the enemy' side. He got his left eye slashed in the process. The Iwa nin turned invisible again cursing in pain.

"Kakashi! So you decided to join the fun after all?" Obito said sarcastically as Kakashi leaned on the tree and pulled out the medic kit that Rin gave him earlier to congratulate him on his Jonin promotion.

"Watch for the enemy damn it!" Kakashi yelled as he started to wrap his eye in bandages.

Obito turned around and planted a kunai in the heart of the enemy not realizing that his Sharingan had awakened.

"How? What's with your eyes? Bastard." These were the last words of the Iwa nin as he fell to the ground dead.

"We heard some commotion, are you two alright?" Nagato asked as team Ame landed on the tree branch with Kakashi and Obito.

"What took you so long?" Obito to asked angrily.

"We were searching for an entrance, and we found one." Nagato said pointing towards the rock dome.

"I think Konan should stay here with Kakashi and tends to his wound. While you Obito and I go to retrieve Rin." Yahiko said to Nagato.

"Yahiko is right. Kakashi isn't going to be much help with that bleeding wound, and Konan knows basic medic jutsu. Besides there's one of him and three of us, this should be pretty easy." Nagato said.

After a small debate the five shinobi came to decision. The decision being that that plan was the correct course of action. So Nagato, Yahiko, and Obito moved in to confront the enemy nin and rescue Rin.

The three entered the Rock dome and immediately saw Rin sitting tied up and staring off into space, no light in her eyes. "Kai!" Obito yelled as he put his hand on her shoulder, breaking the Genjutsu that she had been placed under.

"You shouldn't have come here." Rin said looking up at her saviors.

"We couldn't just leave you here at the mercy of the enemy Rin." Obito said lifting her up and cutting the ropes that bound her.

"Run idiots! It's a trap!" Rin yelled as the rock dome began to collapse on top of them.

"Shinra Tensei!" Nagato yelled out as the pieces of the rock dome flew outward into the forest.

"Damn it! I thought for sure that would kill those fuckers." The remaining Iwa nin said as he pulled out a ninjato and took up a defensive stance.

Within seconds Yahiko was upon him, his hands growing, and his shin turning grey. The Iwa nin tried to block a punch that was aimed towards his stomach with his blade. This resulted in his ninjato scattering and him flying into a nearby tree. He then looked up to see Nagato who had removed his cloak, and shirt yell. "Armor of the Asura Path!" Nagato then began to transform, several mechanical markings began to appear on his body, he grew four extra arms as well as two extra faces in the sides of his head, and a long serrated blade grew out of his back from right under his shoulder blades. Meanwhile Yahiko completed his transformation. Yahiko's hands were about four times their normal size and had sharp claws, all of his skin was a dark grey color, his eyes became black with yellow irises, three horn like protrusions grew from his forehead, he grew a tail, and his back grew long spikes along his spine all the way down his tail.

"MONSTERS! GET AWAY FROM ME!" The Iwa nin screamed in fear before he died via Nagato's blade tail piercing his head.

"We're not done yet, I sense about a hundred chakra signatures approaching and we aren't expecting backup. Hide kids this is going to get ugly." Yahiko said transforming his hands, first he grew several extra fingers from random areas of his hands, and then his fingers opened up into a hollow honeycomb pattern.

"So crowd control techniques then." Nagato said opening his arms up to reveal hundreds of tiny missiles.

Several Iwa shinobi charged out of the woods only for the last words they ever heard to be "Sōkai Enpō!" (Twin Mystic Flame Cannons). As Yahiko began pelting them with golden flames imbued with sage chakra. They died upon contact with the flames, as it burns their chakra system. More tried attacking from behind Yahiko only for Nagato to neutralize them by firing several missiles at them. The rest of the battle was short since most of the remaining enemies retreated due to the sheer amount of destruction that the two in front of them are capable of.

Meanwhile Konan hid herself and Kakashi by blending in with the tree using paper. She had heard the enemies close in and decided to set a trap for the ones that retreated. She made several paper clones that littered the area with motion sensing paper bombs that were almost impossible to see. About sixty percent of the retreating enemies fell into this trap, leaving less than ten enemies to escape. The Konoha shinobi then completed their objective without any more enemy resistane.

* * *

3 month until the Kyubi attack.

* * *

The Third Shinobi World War was dying down, but that's the most dangerous time in a war between ninjas. Last resort methods start being used, methods that could lead to the destruction of entire nations.

"I'm telling you two you have to kill me." Rin said to her teammates.

"No Rin I can't do it." Obito said looking her in the eyes.

"I agree, Tell us what's wrong. What did they do to you?" Kakashi known on the battlefield as 'the One Eyed Fang' was worried.

"I can't, I mean I literally can't tell you. Part of it makes me unable to tell you. Just know if I go back to Konoha then it's all over. If you hadn't stopped them when you did I wouldn't even know what they did." Rin said trying to get her teammates to understand her predicament.

"Obito, I think that it's either a Genjutsu placed on her, or hypnotic suggestion. Your Sharingan should be able to break either." Kakashi said looking at his best friend.

"Why didn't I think of that?" Obito asked face-palming.

"Because you're an idiot." Kakashi said smiling under his mask.

"Hey!" Obito yelled causing Rin to giggle at her team's antics. "Okay Rin, I just need to say this just in case this doesn't go as planned. I love you, I always have, you don't have to say anything yet, I know you have feelings for Kakashi. I just wanted you to know." Obito said before activating his Sharingan while looking her in the eyes, causing her to freeze in place.

"Well?" Kakashi asked

"It's hypnosis. Not just on her either." Obito said not breaking eye contact.

"What do you mean?" Kakashi was confused.

"It looks like they made her a Jinchuriki for the Sanbi." Obito kept at it. "This is going to take a while, keep us safe Kakashi." Obito said before freezing like Rin.

"Well, looks like the fake pursuers are here." Kakashi said pulling out his tanto.

* * *

Two Hours Later

* * *

Rin gasped for air as Obito passed out from Chakra exhaustion. It took everything in him to undo the hypnosis on Rin and the Biju within her.

"Great, now we have to carry this idiot back to the village." Kakashi said sitting atop a rock with a pile of corpses next to it.

"No, I'll carry him. It's the least I can do." Rin said with a soft smile.

"Does this mean that you." Kakashi was cut off.

"Yes Kakashi. I was a fool not to realize how he felt, and an even bigger fool not to feel the same." Rin said leaning Obito on her shoulder. She struggled to move, so Kakashi helped support Obito as they made their way home.

* * *

Back at Konoha in the Hokage's Office

* * *

"So Kiri shinobi kidnapped Rin, sealed the Sanbi in her, and hypnotized both her and the Sanbi to destroy the village when she entered it. You two stopped it before the hypnosis on her was finished, and Obito undid all of it with his Sharingan." Minato the newly appointed Yondaime Hokage said not the least bit surprised that they would resort to this type of attack. He was surprised however that his student was able to reverse the hypnotism.

"Yes sensei. That is exactly what happened." Kakashi said.

"Rin let me take a look at your seal. It might not be stable just in case something like this happened." Minato said concerned for his student's welfare, as well as the welfare of the village.

"That won't be necessary, Isobu, the Sanbi, isn't going to be a problem as long as I take plenty of naps. He's actually a lot like a Nara, it's easier for him to not try to break out of the seal than it is for him to be hunted down and resealed." Rin said smiling.

"Still I want to make sure that it isn't going to just disappear on you." Minato said.

After taking a look at her seal, he applied some reinforcements to make sure that it didn't just break for no reason.

 **AN: For anyone wondering yes Kurama and Isobu are both going to be at least cooperative, if not friendly latter on. Also Yes Obito and Rin both survived, no Kakashi isn't getting a Sharingan his thing now is more or less surpassing his father while carrying on the legacy of the fang of Konoha, and now Konoha has two Jinchuriki. Next chapter will be hard to write so it might take a while.**


	3. Attack on Konoha

Minato Grunted as he pumped chakra into the seal containing Kurama.

"Suck it up boy, you're not the one giving birth. A man couldn't survive this kind of pain." Biwako said to the Hokage.

"Minato sensei we've got a problem!" Kakashi yelled through the open window.

"What's going on?" Minato asked his student.

"We're under attack, whoever they are they brought an army." Kakashi yelled as something hit him slamming him into the wall.

"Peace was just declared earlier today, the war is over! Whoever it is isn't going to have a village by the end of this!" It is very hard to anger the Yondaime Hokage, but this did the job. "Sensei, take care of thing here for a minute. I'll be back in a flash." Minato said to Jiraiya before he teleported away.

The scene outside was hectic to say the least. It smelled like a graveyard, and an army of white humanoid creatures with green hair were attacking Konoha. Their main target seemed to be the cabin that Kushina was giving birth in though, which made almost didn't make sense, unless they were after Kurama.

Minato pieced their goal together in seconds, he then returned to his wife. When he entered the cabin what he found was enough to drive any mad over the edge. One of the creatures had his son. This one was slightly different though. Its left half was completely pitch black, it had two large plant like protrusions coming from its shoulders, and it had a pair of Sharingan eyes.

"Move at all and this infant dies." It said holding.

Kushina started screaming as Kurama was ripped from her stomach. **"No! Not again! I refuse to let those eyes control me again!"** Kurama yelled as he was being pulled from his container.

Outside was a complete warzone, Nagato, Yahiko, Konan, Rin, and Obito were tearing through enemies left and right. Nagato was in his Asura form, Yahiko was in his mutated sage form, while Rin was in her version 2 cloak with two tails out. Each of the attacking creatures was weak enough for a skilled Genin to take down with relative ease, the problem was their numbers. There were a few thousand of these things, the entirety of Konoha's Shinobi Corps was having trouble keeping them out of the village. Some managed to make through a hole in the wall that some had made via self-detonation. Those that made it in however were swiftly dealt with by the Uchiha Military Police. Just when things seemed under control all of the creatures stopped in their tracks and began retreating. The reason became clear a moment later when a worse than worst case scenario for those who knew about Kushina's burden came true. Not only was Kurama out, but his eyes shown the Sharingan, meaning that he was possessed by someone with a Sharingan.

* * *

With the front line fighters

* * *

"Guys! Minato sensei told me to have Nagato, and Rin hold the Kyubi back for a little while. He's preparing to re-seal it and needs time! Yahiko, Obito, and Konan you three are with me. We have to fight the one controlling the Kyubi." Kakashi shouted as he landed between Obito and Rin.

"Isobu, let's go!" Rin yelled before transforming into the Sanbi, prepared to square off with Kurama.

"Kuchiyose no Jutsu!" Nagato shouted summoning his twin headed dog along with the giant drill-beaked bird.

Meanwhile Kakashi led the others back to the cabin that was now a pile of rubble. "Our target was last sighted here. Do any of you have any tracking skills?" Kakashi was all business when he spoke.

"I can see some residual chakra signatures, one of them belongs to Kushina-san, another to Sensei, the other is unknown." Obito said looking closely with his Sharingan.

"Where does it go?" Kakashi asked.

"Into the ground deeper than I can see, let's see it I can fix that." Obito said before making a few hand signs and performing the Moguragakure no Jutsu. He shot into the ground searching franticly for their target.

A few moments later Obito resurfaced dragging out the half black creature that possesses the Sharingan. The creature immediately went on the offensive firing off a Hōsenka no Jutsu, only for it to be countered by Yahiko's Sōkai Enpō (Twin Mystic Flame Cannons). Next it attempted to flee underground before it had its chest pierced where it's heart would've been y Kakashi's tanto. Konan then proceeded to coat the creature with paper after Kakashi pulled his tanto out. Konan threw it into the air before Yahiko sliced it into four pieces using claws that merged to form a blade like structure on the end of his hand as he shouted "Kaishu Jinsō!"(Blade Nails of the Mysterious Hand). The fight was far from over though since the black half attached to another one of the creatures transferring the Sharingan along with the plant like protrusions.

* * *

Back with the Biju/summon fight.

* * *

 **"** **Rin I don't know how long we can keep this up! Kurama was always the strongest of my siblings, we're lucky to have trapped him for this long!"** Isobu shouted inside Rin's mind.

"Just a little longer!" Rin replied as Kurama smashed through the Coral Dome that previously trapped him with a Bijudama. Rin, and Isobu took the brunt of the blast that made it passed the Coral Dome, redirecting most of the blast away from the village. The small portion of the blast that did make it through blew an entire sector of the village away though.

Nagato's dog summon which had to this point been split into twenty different beasts attacked Kurama from behind, two latched onto each tail, while one grabbed his neck, the other grabbed his leg, dragging the Biju to the ground. Rin and Isobu then jumped on top of Kurama holding him down for the time being.

* * *

Back with Kakashi and the others.

* * *

"This is getting us nowhere fast! We need to destroy its eyes, or put it under an even stronger Genjutsu than it's using in the Kyubi." Obito yelled at his comrades trying to formulate a plan.

"What about breaking its concentration, can that work?" Konan asked the younger boy.

"No, it's using an Uchiha hidden Genjutsu, one that requires the Sharingan, it will stay until either the Sharingan that applied it is destroyed, the user is killed, or the user releases it. If I can overpower his Sharingan then I can force this thing to release it, but it has a fully matured Sharingan while mine is only fully matured in one eye. I can try, but it needs to stay still long enough for me to make direct eye contact for a few seconds." Obito responded.

Having heard this Yahiko, Konan, and Kakashi sprang into action. Yahiko went for a frontal assault hoping to distract the creature with a flurry of punched and kicks. Konan took the opportunity to wrap it in a foot of chakra enhanced paper before Kakashi shouted "Tajū Doryūheki!" causing two walls of dirt to pop out of the ground before they converged upon the target effectively binding it in place.

"Now Obito!" The other three shouted in unison

Upon hearing this hearing this Obito shunshined in front of the enemy looking deep into its eyes. As the two sets of Sharingan met they began spinning. A few moments later Obito screamed in pain before gripping his eyes which were bleeding profusely. "MY EYES!" He screamed as he fell to the ground writhing in pain.

"Obito!" Kakashi yelled before Konan leapt to his side and began using her paper to bandage his eyes.

"That boy has much potential, to be able to disrupt a Genjutsu cast by the eyes of Madara Uchiha is no small feat. It's almost a shame that his eyes are probably destroyed after tonight." The creature spoke in an inhuman voice that sounded like a mashup of four or five different voices.

"It talks!" Yahiko yelled in surprise since none of the shinobi present had heard their foe talk and didn't know that it had the capacity to do so.

"Yes I do. It seems my mission was a failure, so until next time young ones. I do hope you get stronger before we meet again, this was barely a warm-up. For future reference you may call my brethren and I Zetsu." The creature now identified as a Zetsu said before it tore through the paper and walls of dirt with what appeared to be tree roots. This took the shinobi by surprise, this thing just used Mokuton.

* * *

Back to the Battle of the giants

* * *

The Sharingan in Kurama's eyes faded before his consciousness began to follow. Before he passed out he managed to say **"Bring Kushina here. If I can get back into her seal swiftly enough it may save her life."**

"Rin can you and Isobu Carry him?" Nagato asked.

"For a short distance. That fight took a lot out of the big guy and me." Rin said as she and Isobu picked up Kurama's unconscious body.

Nagato began flying in the direction that he sensed Kushina and Minato. His expression suddenly became one ok shock as Kushina's chakra signature started getting weaker by the second. "Hurry, Nee-chan's dying!" Nagato shouted as they picked up the pace.

They arrived at the same time as the Zetsu suppression team only to see a horrific sight. A Zetsu whose body liked as if it were made of twisted roots decapitating Kushina. It turned to face them and began to speak in a goofy voice. "Hello there. Can you people satisfy my curiosity? I want to know what it's like to be human, and one question keeps coming up. How does it feel to poop?" It had to dodge an onslaught of attacks made by several enraged shinobi. It began mumbling about something as it fazed into the ground. Retreating it said "Maybe next time then?"

"NEE-CHAN!" Nagato screamed as he ran to her corpse cryng. He quickly activated the Powers of the Naraka Path, summoning the head of the King of Hell. It took Kushina's body, and her severed head into its mouth and chewed them a few times before it spat them back out attached to one another, her body was good as new even though she was still dead. Nagato then picked up her body and held it close as he cried out.

The shinobi present looked around for a second unsure of how to comfort their comrade before they seen the Shinigami appear next to Minato before it grabbed Kurama and began cramming it into his newborn son. They rushed to the now dying Hokage, except Obito who couldn't see to make it all the way there and tripped over a candle at the alter that a newborn child was laying on. The infant began crying alerting the shinobi to his presence.

"Bring me my son." Minato said weakly, it was clear that he only had a few minutes to live if he was lucky. Kakashi quickly fetched the infant and Obito and brought them to Minato. "Thank you." Minato said as he removed his coat and began swaddling his son with it. "I'm sorry Naruto, for not being there, for your burden, and for not being able to save your mother. I Hope that one day you'll understand, and maybe you'll be kind enough to forgive this fool for the problems that he's caused you." Naruto stopped crying and fell asleep in his father's arms.

"Kakashi, Obito, Rin, I'm proud of you three. You've all grown into fine shinobi, and I'm glad to have been your sensei. Kakashi, you've learned the importance of your comrades, and what it truly means to be a shinobi. Obito, you don't let anything stop you from achieving your goals, maybe one day you'll become a fine Hokage. Rin, even after having a Biju forced into you you're still training to become a greater medic than Tsunade, I'm sure you will soon enough. Nagato, Yahiko, Konan, You three are some of the greatest people, and shinobi that I know. Don't let this night stop you from becoming even greater people, or shinobi." Minato said, his voice was getting weaker by the second.

"What happened here Minato?" Hiruzen Sarutobi asked as he landed next to the group.

"I'm sorry, I don't have time to explain. I have two more orders as Hokage to give, first Hiruzen I'm sorry that I have to do this to you, but you have to take the seat of Hokage back until someone else is ready to take it up, and my last order goes out to everyone present, please look after my son. Make sure he grows up knowing love, that he knows that I didn't want things to turn out this way, and protect him from those who would seek to end him for being my son. This child, my child, holds a burden greater than the Kyubi on his shoulders. The Shinigami has shown me this. He is…" Minato Namikaze, the Yondaime Hokage wasn't able to finish his sentence before succumbing to the Shinigami's pull. Naruto woke up and began crying even louder than ever. That's when a very small version of Kurama jumped out of the infant's stomach and grabbed him with his tails, he then proceeded to rock the baby asleep.

"What the hell are you doing?" Kakashi asked.

 **"** **I heard Kushina's last thoughts before she was murdered. She asked me to watch over her son, and I intend to do just that."** Kurama said.

"How are you out?" Rin asked, Isobu couldn't do that, so she was curious.

 **"** **Part of the seal that Minato used. This way I can better protect Naruto. He suspect that he will need it once Iwa figures out that Naruto is his son."** Kurama said bringing up a great point.

"They won't figure it out! As Hokage I'm labeling Naruto's heritage an S class secret." Hiruzen said before Nagato put his hand on his shoulder.

"Hokage-sama, we have a lot to talk about. Why don't we wait until tomorrow before we make any decisions regarding Naruto-kun?" The young Uzumaki said making a face that made the old man's heart skip a beat.

"I think you're right, we've got to talk to the council first. I'll let them decide as a whole regarding Naruto-kun. Then first thing in the morning I'll address the village." Hiruzen said reminded of both Mito, and Kushina. He came to the conclusion that it is an Uzumaki thing before he took Naruto from Kurama and began walking to the council. Nagato followed him, being the new representative of the Uzumaki he needed to attend.

* * *

At the Council Meeting

* * *

"Where is the Yondaime? Why is this infant here? This is a serious matter. For that matter why in Nagato-san here rather than his sister?" One civilian asked rapid fire questions, only to be shut up by a blast of killing intent by the entire Shinobi council.

"There are many reasons why things are the way that they are tonight. First I regret to inform you that the Yondaime is no longer with us." Hiruzen said causing a massive uproar. "SILENCE! The second to last order that he gave was for me to take up the hat once more until a suitable successor is found. Next order of business is this child. He is the new container of the Kuybi." Another uproar, many called for the infant's death. Even though the Kyubi hadn't gotten into the village, it did still cause significant damage to the village during the fight to keep it out.

 **"** **Shut up Ningen I was under a Genjutsu put on me by some creature that possessed the eyes of none other than Madara Uchiha! It was a deliberate attempt to steal my powers and use them against the village again! I made a promise to this child's parents upon their dying breaths that I would protect him as if he were my own, anyone who attacks him will find themselves living impaired."** Kurama said as his chibi form popped out of the infant's stomach.

"We were there, the Biju speaks the truth. This creature he speaks of identified itself as well as the others that attacked tonight as Zetsu. It possessed a set of Sharingan that it claimed to belong to Madara Uchiha, if Obito hadn't broken the Genjustu then Kurama here would've gotten to the village and leveled it." Kakashi said as he and the rest of the shinobi who played a major role in the night's events shunshined into the room.

"Anyway back to the matter at hand, tonight's events will be discussed in detail after this order of business. This child was born of Minato Namikaze and Kushina Uzumaki, both of which perished in tonight's events. This leaves us with a decision to make. Do we let it be known who his parents are, or do we keep it secret until he comes of age to claim his inheritance?" Hiruzen interrupted the current discussion in favor of getting this out of the way.

"I say we keep it secret, letting it be known would be like painting a target on his head." Fugaku Uchiha said trying to be sensible even though it would pain him to see his former teammate's son grow up in an orphanage.

 **"** **Let the attackers come, if they managed to sneak past the village gate's sensors, ANBU, Nagato, Konan, Yahiko, Kakashi, Obito, Rin, and my brother's they would be facing me. I may be weakened now, but I'm still more powerful than everybody in this room combined, excluding Isobu of course. To get to this child they would have to send seven nations worth of troops in order to even get close to the boy."** Kurama said growling.

"As much as I hate foxes this one has a point. Wouldn't it be damaging to him to not know who his parents are for sixteen years. Keeping his heritage secret would also mean he couldn't live with Nagato, it could possibly kill his trust in the Hokage, and by extension the village. This plan runs the risk of creating a rouge Jinchuriki, the most dangerous type of nukenin with how strong they are known to be, especially in this ones case since the Biju within can roam free. I say we let the world know, and if assassins come we send a message of their heads in a scroll back to their village of origin. We take care of our own here damn it!" Tsume Inuzuka had a hard time not shouting her proclamation to the heavens.

One by one the entirety of the shinobi council began to agree with Tsume. Once the Nara clan joined the side of the Inuzuka clan all the others fell in immediately, including the Uchiha. The civilian council reluctantly agreed after the basics of sealing were explained to them by Hiruzen, basically how sealing a kunai in a scroll doesn't turn the scroll into a kunai. A few civilian councilmen didn't believe Hiruzen about Naruto not being the Kyubi though, as long as they didn't attempt any direct harm to the boy they would be fine.

"So it's decided, tomorrow during my address to the village young Naruto-kun's heritage will be revealed to the world. Now is the time to go over tonight's events and formulate a plan so that these events don't repeat themselves in the future."

* * *

 **AN: First off a general rule of thumb regarding Zetsu(s?), white=beaten by Yamcha from bragonball, Spiral=nearly Kage level, Black=almost as strong as Madara. Next a couple questions that I intend to answer before they're asked. Yes Obito's eyes have been destroyed function wise, no this is not permanent but it needed to happen for my plans revolving around the Uchiha massacre which will still happen, just very differently.**


	4. I'm Sorry

I remember saying that I was back, and I'm sorry for metaphorically dying again. But I have my reasons. My mom got cancer, and if that wasn't enough I've had to make quite a few adjustments to my life style. You see life's almost never fair, and it's other people who make it that way. Three men with bats and knives took something from me that can't be returned. I'm talking about the use of my legs. The saddest thing about the whole ordeal is that people watched it happen and did nothing, I only made it to the hospital six blocks away because of the kindness of a homeless veteran. My depression about the whole thing has taken away my will to write, or do much of anything anymore. Hell I can barely even read fan fiction anymore, I'm just too depressed to be creative. If I ever get better enough to continue my two stories that I have going then I will, but Consider them both up for adoption. PM me if you're interested. I don't know if I'll return to writing any time soon or ever for that matter, but I hope some interested soul will finish what I started.


End file.
